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Frontiers in Microbiology 2023sp. PT13 is a wild strain with multiple predatory properties that prey on multiple model microorganisms preserved in the laboratory. However, the lysis spectrum of PT13...
INTRODUCTION
sp. PT13 is a wild strain with multiple predatory properties that prey on multiple model microorganisms preserved in the laboratory. However, the lysis spectrum of PT13 on typical soil bacteria and its driving effect on soil microecosystems are still unclear.
METHODS
In this study, the lawn predation method was used to determine the predation diameter of 62 typical soil bacteria by myxobacteria PT13 and analyze their lysis spectra.
RESULTS AND DISCUSSION
The results showed that PT13 had a predation diameter greater than 15 mm against typical soil microorganisms such as , , , , and and had an outstanding lysis effect but a significant preference ( < 0.05). Absolute high-throughput sequencing results showed that PT13 predation drove the microcosmic system composed of 16 bacterial genera, with a significant decrease in the Shannon index by 11.8% (CK = 2.04, = 1.80) and a significant increase in the Simpson index by 45.0% (CK = 0.20, = 0.29). The results of principal coordinate analysis (PCoA) showed that myxobacterial addition significantly disturbed the microcosmic microbial community structure (ANOSIM, < 0.05). LEfSe analysis showed that the relative and absolute abundances (copy numbers) of , , , and decreased significantly very likely due to myxobacterial predation ( < 0.05). However, the predatory effect of PT13 also increased the relative or absolute abundances of some species, such as , , and . It can be concluded that PT13 has a broad-spectrum lysis spectrum but poor cleavage ability for , and the interaction between complex microorganisms limits the predation effect of PT13 on some prey bacteria. This in turn allows some prey to coexist with myxobacteria. This paper will lay a theoretical foundation for the regulation of soil microecology dominated by myxobacteria.
PubMed: 37378286
DOI: 10.3389/fmicb.2023.1211756 -
Microorganisms Mar 2022Ozone is a typical hazardous pollutant in Earth's lower atmosphere, but the phyllosphere and its microbiome are promising for air pollution remediation. Despite research...
Ozone is a typical hazardous pollutant in Earth's lower atmosphere, but the phyllosphere and its microbiome are promising for air pollution remediation. Despite research to explore the efficiency and mechanism of ozone phylloremediation, the response and role of the phyllosphere microbiome remains untouched. In this study, we exposed to different ozone levels and revealed microbial successions and roles of the phyllosphere microbiome during the exposure. The low-level exposure (156 ± 20 ppb) induced limited response compared to other environmental factors. Fungi failed to sustain the community richness and diversity, despite the stable ITS concentration, while bacteria witnessed an abundance loss. We subsequently elevated the exposure level to 5000~10,000 ppb, which considerably deteriorated the bacterial and fungal diversity. Our results identified extremely tolerant species, including bacterial genera (, , and ) and fungal genera ( and ). Compositional differences suggested that most core fungal taxa were related to plant diseases and biocontrol, and ozone exposure might intensify such antagonism, thus possibly influencing plant health and ozone remediation. This assumption was further evidenced in the functional predictions via a pathogen predominance. This study shed light on microbial responses to ozone exposure in the phyllosphere and enlightened the augmentation of ozone phylloremediation through the microbial role.
PubMed: 35456732
DOI: 10.3390/microorganisms10040680 -
Frontiers in Microbiology 2021Unlike for vertebrates, the impact of starvation on the gut microbiome of invertebrates is poorly studied. Deciphering shifts in metabolically active associated...
Unlike for vertebrates, the impact of starvation on the gut microbiome of invertebrates is poorly studied. Deciphering shifts in metabolically active associated bacterial communities in vertebrates has led to determining the role of the associated microbiome in the sensation of hunger and discoveries of associated regulatory mechanisms. From an invertebrate perspective, such as the black soldier fly, such information could lead to enhanced processes for optimized biomass production and waste conversion. Bacteria associated with food substrates of black soldier fly are known to impact corresponding larval life-history traits (e.g., larval development); however, whether black soldier fly larval host state (i.e., starved) impacts the gut microbiome is not known. In this study, we measured microbial community structural and functional shifts due to black soldier fly larvae starvation. Data generated demonstrate such a physiological state (i.e., starvation) does in fact impact both aspects of the microbiome. At the phylum level, community diversity decreased significantly during black soldier fly larval starvation ( = 0.0025). Genus level DESeq2 analysis identified five genera with significantly different relative abundance ( < 0.05) across the 24 and 48 H post initiation of starvation: , , , , and . Finally, we inferred potential gene function and significantly predicted functional KEGG Orthology (KO) abundance. We demonstrated the metabolically active microbial community structure and function could be influenced by host-feeding status. Such perturbations, even when short in duration (e.g., 24 H) could stunt larval growth and waste conversion due to lacking a full complement of bacteria and associated functions.
PubMed: 33664713
DOI: 10.3389/fmicb.2021.601253 -
Frontiers in Microbiology 2024Bacterial degradation mechanism for high chlorinated pentachlorobiphenyl (PentaCB) with worse biodegradability has not been fully elucidated, which could limit the full...
Bacterial degradation mechanism for high chlorinated pentachlorobiphenyl (PentaCB) with worse biodegradability has not been fully elucidated, which could limit the full remediation of environments afflicted by the complex pollution of polychlorinated biphenyls (PCBs). In this research, a new PentaCB-degrading bacterium that has not been reported was obtained using enzymatic screening method. The characteristics of its intracellular enzymes, proteome and metabolome variation during PentaCB degradation were investigated systematically compared to non-PentaCB conditions. The findings indicate that the degradation rate of PentaCB (1 mg/L) could reach 23.9% within 4 hours and achieve complete degradation within 12 hours, with the mixture of intracellular enzymes being most effective at a pH of 6.0. During the biodegradation of PentaCB, the 12 up-regulated proteins characterized included ABC transporter PentaCB-binding protein, translocase protein TatA, and signal peptidase I (SPase I), indicating the presence of functional proteins for PentaCB degradation in both the cytoplasm and the outer surface of the cytoplasmic membrane. Furthermore, five differentially enriched metabolites were strongly associated with the aforementioned proteins, especially the up-regulated 1, 2, 4-benzenetriol which feeds into multiple degradation pathways of benzoate, chlorocyclohexane, chlorobenzene and aminobenzoate. These relevant results help to understand and speculate the complex mechanisms regarding PentaCB degradation by , which have both theoretical and practical implications for PCB bioremediation.
PubMed: 38933025
DOI: 10.3389/fmicb.2024.1389805 -
Frontiers in Microbiology 2022Genetic and functional characteristics of rice leaf endophytic actinobacterial member, are described. Morphotyping, multilocus sequence analysis and transmission...
Genetic and functional characteristics of rice leaf endophytic actinobacterial member, are described. Morphotyping, multilocus sequence analysis and transmission electron microscopy indicated the species identity of the endophytic bacterium, OsEnb-ALM-D18, as . The endophytic showed probiotic solubilization of plant nutrients/minerals, produced hydrolytic enzyme/phytohormones, and showed endophytism in rice seedlings. Further, the endophytic colonization by OsEnb-ALM-D18 was confirmed using reporter gene coding for green fluorescence protein. OsEnb-ALM-D18 showed volatilome-mediated antibiosis (95.5% mycelial inhibition) on . Chemical profiling of OsEnb-ALM-D18 volatilome revealed the abundance of 9-Octadecenoic acid, Hexadecanoic acid, 4-Methyl-2-pentanol, and 2,5-Dihydro-thiophene. Upon endobacterization of rice seedlings, altered shoot and root phenotype suggestive of activated defense. Over 80.0% blast disease severity reduction was observed on the susceptible rice cultivar Pusa Basmati-1 upon foliar spray with . qPCR-based gene expression analysis showed induction of CERK1, PAD4, NPR1.3, and FMO1 suggestive of endophytic immunocompetence against blast disease. Moreover, OsEnb-ALM-D18 conferred immunocompetence, and antifungal antibiosis can be the future integrated blast management strategy.
PubMed: 36619990
DOI: 10.3389/fmicb.2022.1035602 -
ACS Omega Nov 2019Xanthan, a highly stable polysaccharide which is not easily degraded by most microorganisms, contains a cellulosic backbone with trisaccharide side chains composed of...
Xanthan, a highly stable polysaccharide which is not easily degraded by most microorganisms, contains a cellulosic backbone with trisaccharide side chains composed of mannosyl-glucuronyl-mannose attached α-1,3 to alternating glucosyl residues. Different digestion strategies were first applied to demonstrate the complexity about the proteomes of sp. XT11 in xanthan medium and glucose medium. Significantly up-regulated proteins induced by xanthan were screened out by the label-free quantitation of the proteomes of sp. XT11 in xanthan medium and glucose medium. Consequently, 2746 and 2878 proteins were identified in proteomes of sp. XT11 in xanthan medium and glucose medium individually, which represent 80.6 and 84.4% of total protein dataset predicted to be expressed by the gene. In the list of 430 induced proteins containing the proteins specifically expressed or up-regulated in xanthan medium, 19 proteins involved in carbohydrate-active enzymes database and 38 proteins annotated with transporter activity were critical in the degrading pathway of xanthan. Four CAZymes (GH3, GH38, GH9, and PL8) and one ABC transporter (LX1-1GL001097) were verified with quantitative real-time polymerase chain reaction. Four CAZymes (GH3, GH38, GH9, and PL8) were further verified with the enzyme assay. This study suggests a xanthan-degrading pathway in sp. XT11, and other potential xanthan degradation-related proteins still need further investigation.
PubMed: 31763532
DOI: 10.1021/acsomega.9b02313 -
Gut Pathogens Mar 2013The aim of this study is to expand existing knowledge about the CRC-associated microbiome among Han Chinese, and to further discover the variation pattern of the human...
BACKGROUND
The aim of this study is to expand existing knowledge about the CRC-associated microbiome among Han Chinese, and to further discover the variation pattern of the human CRC microbiome across all population.
FINDINGS
Using pyrosequencing-based molecular monitoring of bacterial 16S rRNA gene from eight tumor/normal tissue pairs of eight Chinese CRC patients, we analyzed and characterized the basic features of the CRC-associated microbiome. Firstly, we discovered an increasing diversity among tumor-associated bacterial communities. Secondly, in 50% of Chinese CRC patients, we found a significant increase of Roseburia (P = 0.017), and a concurrent decrease of both Microbacterium (P = 0.009) and Anoxybacillus (P = 0.009) in tumor tissue.
CONCLUSIONS
We discovered a novel CRC microbiome pattern in Chinese. Both the over-represented Roseburia bacteria at tumor sites and the over-represented Microbacterium and Anoxybacillus bacteria away from tumor sites were both closely related in Chinese CRC patients. Across several populations reported in this study and previously, we observed both common and distinctive patterns of human CRC microbiome's association with a high-risk of CRC.
PubMed: 23497613
DOI: 10.1186/1757-4749-5-2 -
Microbiology Resource Announcements Jul 2022The microbacteriophages QuadZero and AnnaLie were isolated from soil samples from Charlotte, NC, and were classified into EA and EB clusters, respectively. QuadZero has...
The microbacteriophages QuadZero and AnnaLie were isolated from soil samples from Charlotte, NC, and were classified into EA and EB clusters, respectively. QuadZero has a 40,140 base-pair double-stranded DNA genome with 62 predicted protein coding genes, whereas AnnaLie has a 41,665-bp genome with 71 predicted protein coding genes.
PubMed: 35658534
DOI: 10.1128/mra.00208-22 -
Applied and Environmental Microbiology Jan 2013Microbacterium sp. 4N2-2, isolated from a wastewater treatment plant, converts the antibacterial fluoroquinolone norfloxacin to N-acetylnorfloxacin and three other...
Microbacterium sp. 4N2-2, isolated from a wastewater treatment plant, converts the antibacterial fluoroquinolone norfloxacin to N-acetylnorfloxacin and three other metabolites. Because N-acetylation results in loss of antibacterial activity, identification of the enzyme responsible is important for understanding fluoroquinolone resistance. The enzyme was identified as glutamine synthetase (GS); N-acetylnorfloxacin was produced only under conditions associated with GS expression. The GS gene (glnA) was cloned, and the protein (53 kDa) was heterologously expressed and isolated. Optimal conditions and biochemical properties (K(m) and V(max)) of purified GS were characterized; the purified enzyme was inhibited by Mn(2+), Mg(2+), ATP, and ADP. The contribution of GS to norfloxacin resistance was shown by using a norfloxacin-sensitive Escherichia coli strain carrying glnA derived from Microbacterium sp. 4N2-2. The GS of Microbacterium sp. 4N2-2 was shown to act as an N-acetyltransferase for norfloxacin, which produced low-level norfloxacin resistance. Structural and docking analysis identified potential binding sites for norfloxacin at the ADP binding site and for acetyl coenzyme A (acetyl-CoA) at a cleft in GS. The results suggest that environmental bacteria whose enzymes modify fluoroquinolones may be able to survive in the presence of low fluoroquinolone concentrations.
Topics: Acetylation; Actinomycetales; Anti-Bacterial Agents; Binding Sites; Biotransformation; Cloning, Molecular; DNA, Bacterial; Enzyme Inhibitors; Escherichia coli; Gene Expression; Glutamate-Ammonia Ligase; Models, Molecular; Molecular Sequence Data; Molecular Weight; N-Terminal Acetyltransferases; Norfloxacin; Recombinant Proteins; Sequence Analysis, DNA; Wastewater
PubMed: 23104417
DOI: 10.1128/AEM.02347-12 -
Plants (Basel, Switzerland) Dec 2020Nowadays, oil crops are very attractive both for human consumption and biodiesel production; however, little is known about their commensal rhizosphere microbes. In this...
Rhizobacteria and Arbuscular Mycorrhizal Fungi of Oil Crops (Physic Nut and Sacha Inchi): A Cultivable-Based Assessment for Abundance, Diversity, and Plant Growth-Promoting Potentials.
Nowadays, oil crops are very attractive both for human consumption and biodiesel production; however, little is known about their commensal rhizosphere microbes. In this study, rhizosphere samples were collected from physic nut and sacha inchi plants grown in several areas of Thailand. Rhizobacteria, cultivable in nitrogen-free media, and arbuscular mycorrhizal (AM) fungi were isolated and examined for abundance, diversity, and plant growth-promoting activities (indole-3-acetic acid (IAA) and siderophore production, nitrogen fixation, and phosphate solubilization). Results showed that only the AM spore amount was affected by plant species and soil features. Considering rhizobacterial diversity, two classes- ( sp. and sp.) and ( sp. and spp.)-were identified in physic nut rhizosphere, and three classes; ( sp.), ( sp.) and ( sp.) were identified in the sacha inchi rhizosphere. Considering AM fungal diversity, four genera were identified (, , , and ) in sacha inchi rhizospheres and two genera ( and ) in physic nut rhizospheres. The rhizobacteria with the highest IAA production and AM spores with the highest root-colonizing ability were identified, and the best ones ( sp. CM1-RB003 and sp. CM2-AMA3 for physic nut, and sp. CR1-RB056 and sp. CR2-AMF1 for sacha inchi) were evaluated in pot experiments alone and in a consortium in comparison with a non-inoculated control. The microbial treatments increased the length and the diameter of stems and the chlorophyll content in both the crops. CM1-RB003 and CR1-RB056 also increased the number of leaves in sacha inchi. Interestingly, in physic nut, the consortium increased AM fungal root colonization and the numbers of offspring AM spores in comparison with those observed in sacha inchi. Our findings proved that AM fungal abundance and diversity likely rely on plant species and soil features. In addition, pot experiments showed that rhizosphere microorganisms were the key players in the development and growth of physic nut and sacha inchi.
PubMed: 33327574
DOI: 10.3390/plants9121773